Background
Following mass vaccination campaigns with ACWY conjugate vaccines (2016-2019), an epidemiological shift has been observed. Despite the introduction of the 13-valent pneumococcal conjugate vaccine (PCV 13) since 2014, pneumococcus remains a major causative agent of meningitis epidemics. This epidemiological trend has raised the question of whether these pneumococcal meningitis epidemics are the result of serotypes replacement with the emergence of non-vaccine serotypes.
Aim/Methods
Aiming to understand this epidemiology, we conducted a longitudinal analysis integrating three complementary studies: (1) retrospective 2020-2022 serotyping at Institut National d'Hygiène-Togo, (2) prospective 2025 epidemiological study (January-July) and (3) molecular characterization via cpsB gene sequencing at Institut Pasteur's WHO Meningitis Collaborating Centre. Real-time PCR targeting lytA gene confirmed S. pneumoniae identification; cpsB sequencing and k-mer analysis determined serotypes.
Results
Total samples analyzed: 777 (2020-2022), 487 (2025), and 82 (Institut Pasteur Paris). Key findings document a complete epidemiological transition in bacterial meningitis causative agents. Streptococcus pneumoniae has become dominant bacterial responsible for meningitis with no more isolation of N. meningitidis since 2020. This represents disappearance of the previously dominant meningococcal epidemics (NmA pre-2016, NmW 2016-2017, NmC 2019). During the latest 2025 meningitis outbreak Streptococcus pneumoniae represented 92% of confirmed bacterial meningitis. Serotype 1 remains consistently dominant despite PCV13 coverage: 29.27% (2020-2022), 39.62% (2025 epidemiological), 64% (Institut Pasteur cpsB sequencing). In summary, from 2020 – 2025, the serotypes included in PCV13 that continue to circulate in Togo despite PCV13’s introduction into routine vaccination were (1, 3, 4, 19F, 19A, 18C, 23F), in addition to the non-PCV13 serotypes (13, 12F/44, 35F/47F, 35B, 15b/15B, 10A, 24F/24A/24B, 16F, 23B, 9L/9N, 33 AF, 11B/11C, 7 CB1).
Conclusion
This longitudinal analysis documents a critical epidemiological transition in Togo: (1) Complete disappearance of N. meningitidis epidemics, confirming vaccination campaign effectiveness; (2) Emergence of S. pneumoniae as dominant causative agent since 2019; (3) Persistent prevalence of vaccine-targeted serotype 1, suggesting potential vaccination escape or incomplete coverage; (4) Significant emergence of non-vaccine serotypes, indicating serotype replacement post-PCV13 introduction. These findings highlight urgent need for enhanced genomic surveillance and adaptation of vaccination strategies, including consideration of higher-valency pneumococcal vaccines (PCV15, PCV20, PCV21).